I would concrete the floor right away. Maybe it was just me, but I parked a couple cars in a graveled pole shed and everything turned to rust.
A 40'x60', 6" slab is 44.44 yards of concrete. Then say you add 340' of footing, consisting of the perimeter, one run down the center length wise and 2 runs on the width, at 24"dx12"w x340', thats another 25.19 yards so 69.63 yards of concrete. Here it is $80 a yard, so $5570 just for the "mud". The going turn key rate here for a slab is $4.50-$5 per sq. foot. which includes the steel (re-bar) so around $11k (here) That alone is a 3rd of your budget. (this is for 3000psi)
Even if you go with a gravel floor, full or partial, you can still pour a concrete floor at a later date. PITA though.
Add a radiant system more $$, so a personal choice there.
This. ^^^^^
I agree, if you can swing it concrete the whole thing. Go as big as your wallet will allow. I have a 30x50 Quonset with a 14' apartment in the back. This leaves a 36x30 shop....way too small. If I had it to do over it would have been a 50x100....sounds crazy, but much more practical for parking equipment, vehicles, & projects like woodworking and welding.
Western, why would you run footers down the center and width? I only have footers on the two load bearing 50' sides, and no problems at all after 4 years. I did use steel mesh, extra fiber, and on the end wall perimeter, I dig a 3' post hole every 8'. I don't think those extra footers will really make much difference at all, unless a car lift is going in there, and then it has to be properly placed.